ScanBious: Survey for Obesity Genes Using PubMed Abstracts and DisGeNET

Tarbeeva, Svetlana; Lyamtseva, Ekaterina; Лисица, А. В.; Kozlova, Anna; Ponomarenko, Elena A.; Ilgisonis, Ekaterina V.

doi:10.3390/jpm11040246

Cited by 4 publications

(5 citation statements)

References 37 publications

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“…The research was performed using a combination of automatic text-analysis algorithms, ScanBious [ 16 , 17 ] and biocuration [ 18 ]. The automatic text-analysis algorithms used in this work have previously shown their effectiveness for reconstructing metabolic pathways [ 19 ], assessing the current state of the selected subject area [ 20 ], and investigating trends in scientific research in the field of biomedicine [ 21 ]. The PubMed/MEDLINE library of scientific publications in biology and medicine was used as a data source [ 22 ].…”

Section: Methodsmentioning

confidence: 99%

“…Each article was associated with a set of keywords (MeSH (Medical Subject Heading) terms) assigned by the curators of the resource for indexing and briefly characterizing the content of each publication. ScanBious is a free-ware Web-system for highlighting key concepts revealed from PubMed abstracts and related MeSH terms; it provides an interface to the transparent algorithm, which relies on the co-occurrence of two terms in one abstract [ 20 ]. One can make a search query to ScanBious and get a list of relevant articles similar to the PubMed/MEDLINE system.…”

Section: Methodsmentioning

confidence: 99%

“…Unlike PubMed/MEDLINE, the user can process the obtained set of publications: select the most relevant to the search query articles and their abstracts, extract their MeSH terms, select target MeSH terms, and visualize them as a semantic network based on the measure of interrelation (Jaccard index). The nodes of the semantic network are the objects (MeSH terms) selected by the user and the links of which are a list of publications in which both objects are described [ 20 ]. The size of the nodes reflects the number of publications; the thickness and the color of the edge–Jaccard’s index.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Food for Thought: Proteomics for Meat Safety

Tarbeeva

Kozlova

Sarygina

et al. 2023

Life

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Foodborne bacteria interconnect food and human health. Despite significant progress in food safety regulation, bacterial contamination is still a serious public health concern and the reason for significant commercial losses. The screening of the microbiome in meals is one of the main aspects of food production safety influencing the health of the end-consumers. Our research provides an overview of proteomics findings in the field of food safety made over the last decade. It was believed that proteomics offered an accurate snapshot of the complex networks of the major biological machines called proteins. The proteomic methods for the detection of pathogens were armed with bioinformatics algorithms, allowing us to map the data onto the genome and transcriptome. The mechanisms of the interaction between bacteria and their environment were elucidated with unprecedented sensitivity, specificity, and depth. Using our web-based tool ScanBious for automated publication analysis, we analyzed over 48 000 scientific articles on antibiotic and disinfectant resistance and highlighted the benefits of proteomics for the food safety field. The most promising approach to studying safety in food production is the combination of classical genomic and metagenomic approaches and the advantages provided by proteomic methods with the use of panoramic and targeted mass spectrometry.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Food for Thought: Proteomics for Meat Safety

Tarbeeva

Kozlova

Sarygina

et al. 2023

Life

Self Cite

View full text Add to dashboard Cite

show abstract

“…The primary analysis in this study is performed using a text-mining tool to highlight and select concepts from the PubMed ScanBious source ( , accessed on 25 November 2021) [ 6 , 7 ]. Additionally, we analyze the literature from the past ten years and use secondary literature sources.…”

Section: Introductionmentioning

confidence: 99%

A Recent Ten-Year Perspective: Bile Acid Metabolism and Signaling

et al. 2022

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Bile acids are important physiological agents required for the absorption, distribution, metabolism, and excretion of nutrients. In addition, bile acids act as sensors of intestinal contents, which are determined by the change in the spectrum of bile acids during microbial transformation, as well as by gradual intestinal absorption. Entering the liver through the portal vein, bile acids regulate the activity of nuclear receptors, modify metabolic processes and the rate of formation of new bile acids from cholesterol, and also, in all likelihood, can significantly affect the detoxification of xenobiotics. Bile acids not absorbed by the liver can interact with a variety of cellular recipes in extrahepatic tissues. This provides review information on the synthesis of bile acids in various parts of the digestive tract, its regulation, and the physiological role of bile acids. Moreover, the present study describes the involvement of bile acids in micelle formation, the mechanism of intestinal absorption, and the influence of the intestinal microbiota on this process.

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“…The review purposed to assess the current state of the eating behavior of athletes, food market development, food choice rationality, and effectiveness of the developed and elaborated recommendations. The primary analysis was performed using a text-mining tool to highlight and pick up concepts from the PubMed ScanBious source (https://cryptome.ru/, accessed on 15 September 2021) [17,18]. The combined pool of articles of interest was comprised of 94 studies within 10 years depth.…”

Section: Introductionmentioning

confidence: 99%

Sports Nutrition: Diets, Selection Factors, Recommendations

Malsagova¹,

Kopylov²,

Sinitsyna³

et al. 2021

Nutrients

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An athlete’s diet is influenced by external and internal factors that can reduce or exacerbate exercise-induced food intolerance/allergy symptoms. This review highlights many factors that influence food choices. However, it is important to remember that these food choices are dynamic, and their effectiveness varies with the time, location, and environmental factors in which the athlete chooses the food. Therefore, before training and competition, athletes should follow the recommendations of physicians and nutritionists. It is important to study and understand the nutritional strategies and trends that athletes use before and during training or competitions. This will identify future clinical trials that can be conducted to identify specific foods that athletes can consume to minimize negative symptoms associated with their consumption and optimize training outcomes.

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ScanBious: Survey for Obesity Genes Using PubMed Abstracts and DisGeNET

Cited by 4 publications

References 37 publications

Food for Thought: Proteomics for Meat Safety

Food for Thought: Proteomics for Meat Safety

A Recent Ten-Year Perspective: Bile Acid Metabolism and Signaling

Sports Nutrition: Diets, Selection Factors, Recommendations

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